水稻株高QTL定位及精确性分析

分别应用具有127和131个标记位点的"广佳"(广陆矮4号×佳辐占)和"明佳"(明恢86×佳辐占)重组自交系群体,利用复合区间作图法(CIM)对水稻株高数量性状位点(QTL)进行检测和效应分析.为保证QTL定位精确性,采用排列试验法确定每一群体的LOD阀值.结果显示:排列测验法是一个十分有效的阀值推断统计方法,两个群体LOD阀值分别为2.8和2.7."广佳"群体共检测到5个加性QTL,位于第1、6、7、8和11染色体的5个区间,单位点贡献率在5.31%～48.35%之间;"明佳"群体共检测到4个加性QTL,位于第3、5、9和12染色体的4个区间,单位点贡献率在7.56%～11.50%之间.同时利用混合线性模型复合区间作图法(MCIM)在两群体各检测到1对上位性QTL.作者从实验设计和数据分析方面对QTL定位精确性进行了讨论,为今后数量性状遗传研究提供有益借鉴.     

改进的复合区间作图模型及在杨树上的QTL定位

复合区间作图法最先是为近交群体而设计的作图方法。林木F₁代群体具有遗传杂合度高,生长周期漫长等特点,很难产生近交系,不能简单的套用适用于近交群体的复合区间作图模型。本文建立了适用于林木全同胞家系的QTL复合区间作图统计模型,运用了“逐步回归法”筛选出最优遗传背景标记。采用Monte Carlo方法模拟全同胞家系中共有6条长100cM的染色体,模拟结果表明,每个QTL的位置和遗传力的计算比较精确。本文利用杨树双亲的SNP分子标记遗传连锁图谱,以及其子代的树高生长性状进行了QTL定位 。当似然比统计量的阀值(对应于 LOD 为3.0)取为11.2时,在母本美洲黑杨的遗传连锁图谱上,有4个 QTL 分布在4个连锁群上 。当似然比统计量的阀值取为 16.5,在父本小叶杨的遗传连锁图谱上, 有 3 个 QTL 分布在3个连锁群上。显示了本文所建复合区间作图统计模型有着明显的QTL作图效力。文中所有的计算都是使用 R语言软件编程完成的。#$NL关键词 复合区间作图,F₁代群体,逐步回归法,Monte Carlo     

玉米株高和穗位高遗传基础的QTL剖析

玉米是世界范围内具有经济重要性的作物之一.株高和穗位高是玉米育种过程中需考虑的2个重要农艺性状,对玉米产量、抗倒伏性及株型等都有较大影响.为进一步明确玉米株高和穗位高的遗传机制,本研究以B73×Zheng58的含有165个株系的F3∶4重组自交系群体为作图群体,利用覆盖玉米10条染色体189个SSR标记对株高和穗位高进行QTL定位分析.总共定位到5个株高QTL和6个穗位高QTL;这11个QTL分布在除2号和6号之外的其他8条染色体上.单个QTL表型变异贡献率的变幅为4.3%~14.2%.其中10个QTL与以前报道过的QTL的位置相近或重叠,而株高QTL(qPH04-01)是新发现的群体专一性的QTL,最靠近标记umc0371,表型变异贡献率为8.8%,是值得进一步研究和利用的位点.     

玉米株高和穗位高遗传基础的QTL剖析（英文）

玉米是世界范围内具有经济重要性的作物之一.株高和穗位高是玉米育种过程中需考虑的2个重要农艺性状,对玉米产量、抗倒伏性及株型等都有较大影响.为进一步明确玉米株高和穗位高的遗传机制,本研究以B73×Zheng58的含有165个株系的F3:4重组自交系群体为作图群体,利用覆盖玉米10条染色体189个SSR标记对株高和穗位高进行QTL定位分析.总共定位到5个株高QTL和6个穗位高QTL;这11个QTL分布在除2号和6号之外的其他8条染色体上.单个QTL表型变异贡献率的变幅为4.3%~14.2%.其中10个QTL与以前报道过的QTL的位置相近或重叠,而株高QTL(qPH04-01)是新发现的群体专一性的QTL,最靠近标记umc0371,表型变异贡献率为8.8%,是值得进一步研究和利用的位点.     

中国小麦周8425B/中国春RIL群体成株抗叶锈基因的QTL定位

为确定小麦叶锈病抗病基因的QTL检测及定位,找到能与抗病基因紧密连锁的分子标记,以小麦品种周8425B,中国春及其杂交获得的244个F_(2∶8) RIL群体为试验材料,分别于2014～2015年在河北保定和河南周口进行了田间叶锈病病害严重度调查,获得了群体的表型数据,利用SNP标记和SSR标记进行基因分型,得到了群体基因型数据,运用软件Joinmap和QTL Ici Mapping 3.1进行连锁作图和QTL定位。结果找到2个QTL位点,分别位于2B,7D染色体上。     

回归法QTL作图效率的分析

通过随机模拟，研究了群体的大小，遗传力和标记区间长度3个因素对回归法QTL作图效率的影响，结果表明：当遗传力一定时，随着群体大小的增加，QTL定位的精度逐渐增加，而加群体的大小一定时，随着遗传力的增加，QTL定位的精确度也逐渐增加，无论群体的大小和遗传力的大小如何，用回归法都能得到群体的平均值，数量性状的性效应和显性效应的精确估计值，当群体的大小和遗传力一定时，回归显性检验统计量F随着标记位点区间长度的增加而减少。     

玉米营养品质性状的QTL定位

以玉米自交系201×698-3的233个F2:3家系为作图群体,利用SSR分子标记构建遗传图谱.采用随机区组设计,分别在四川雅安和德阳进行田间试验,人工套袋自交种子供性状考查,利用区间作图法进行QTL定位分析.构建了具有134对SSR标记的玉米遗传图谱,覆盖整个基因组1831.4cM,平均图距13.67cM.从16个营养品质性状中共检侧到35个QTL,其中影响蛋白质、淀粉和油份含量的有6个QTL,分别位于第1、2、4和8染色体上,单个性状的QTL为1～3个,每个QTL的作用可解释表型变异的8.1%～21.0%;控制赖氨酸等13种氨基酸含量的有29个QTL,分别位于第1、2、4、8、9和10染色体上,单个性状的QTL为1～5个,每个QTL的作用可解释表型变异的3.5%～30.1%.在本群体的营养品质性状QTL中,超显性效应起主导作用,其次为完全显性效应.     

"三系"杂种小麦单倍体加倍群体的构建及其应用分析

用花药培养法构建了1个由43个单株组成的"三系"杂种小麦单倍体加倍(DH)群体,其中21株是可育的,22株不育.对此群体在遗传育种、基因克隆、QTL分析等方面的利用价值进行了分析.     

小麦雌性育性双向极端群体QTL定位策略初探

在极端不育群体中计算重组频率(c值)初步筛选QTL位点的基础之上,利用普通小麦中育性正常的良种藁城8901(P1)与雌性不育系XND126(P2)杂交F2群体中的189株隐性极端不育株和63株极端可育株组成的双向极端群体为定位群体,构建了连锁图,分析定位了小麦雌性育性位点taf1,获得了与F2平衡群体相同的定位位点.分析发现与taf1位点连锁较紧密的标记,其c值较小.利用极端群体的策略能快速有效的定位小麦雌性育性QTL在染色体上的位置.     

小麦品质性状的QTL定位研究进展

本文系统地总结了国内外小麦品质性状QTL定位研究的主要性状、所用群体、标记类型、QTL定位所在的染色体位置及贡献率的大小,提出了小麦品质性状QTL定位中存在的问题,展望了小麦品质性状QTL定位的发展方向。     

Detection of quantitative trait loci and heterotic loci for plant height using an immortalized F2 population in maize

A set of recombinant inbred lines (RIL) derived from Yuyu22, an elite hybrid widespread in China, was used to construct an immortalized F2 (IF2) population comprising 441 different crosses. Genetic linkage maps were constructed containing 10 linkages groups with 263 simple sequence repeat (SSR) molecular markers. Twelve and ten quantitative trait loci (QTL) were detected for plant height in the IF2 and RIL populations respectively, using the composite interval mapping method, and six same QTL were identified in the two populations. In addition, ten unique heterotic loci (HL) located on seven different chromosomes were revealed for plant height using the mid-parent heterosis as the input data. These HL explained 1.26%―8.41% of the genotypic variance in plant height heterosis and most expressed overdominant effects. Only three QTL and HL were located in the same chromosomal region, it implied that plant height and its heterosis might be controlled by two types of genetic mechanisms.     

Dynamic analysis of QTL for plant height at different developmental stages in maize （Zea mays L.）

Plantheightisoneofimportantagronomictraitsinmaizebreeding.Inthepastfewyears,toincreasetheplantingdensityandpreventplantsfromlodging,studiesonthegeneticmechanismofplantheightweregivengreatattentionto.Sincethe1990s,molecularmarkershaveprovidedapowerfultooltostudythetraitofplantheightatthemolecularlevel[1—3].Butmostofresearchforplantheightonlyfocusedondataatmaturestage.Tillnow,about70genesorQTLshavebeenlocated[4].Moreover,somegeneshavebeenevencloned[5—7].Duringthevege-tativegrowthperiod,plant…     

Molecular dissection of plant height QTLs using recombinant inbred lines from hybrids between common wheat （Triticum aestivum L.） and spelt wheat （Triticum spelta L.）

In wheat, plant height is an important agronomic trait, and a number of quantitative trait loci (QTLs) controlling plant height have been located. In this study, using the conditional and unconditional QTL mapping methods, combined with data from five different growth stages over two years of field trials, the developmental behavior for plant height in wheat was dissected. Nine unconditional QTLs and 8 conditional QTLs were identified, of which 6 were detected by both methods. None of the 11 QTLs was detected at all of the 5 investigated developmental stages, but 7 QTLs were detected at certain stages in both years. Further analysis identified 9 unconditional QTLs at different stages, which could explain the phenotypic variation from 4.81% to 17.35%. It was noteworthy that one major QTL designated QHt-4B-2, which was located on chromosome 4B, was detected on May 18 and 25 in both years, and its genetic contributions to plant height ranged from 13.42% to 16.13%. Moreover, of the 8 conditional QTLs identified, six were detected in both years, in the order of QHt-3B→QHt-4B-1→QHt-4B-2→QHt-4D→QHt-5A and QHt-2B expressed at the same developmental stage. The results indicate that QTL expression during plant height development is selective and in a temporal order.     

QTL mapping of resistance to sheath blight in maize（Zea mays L.）

Maize sheath blight (Rhizoctonia Solani) is a widely occurring fungus disease with great harm to corn-pro- ducing regions in the world. The first happening of sheath blight in China was reported in Jilin Province as early as in 1966[1]. Since the 1970s, the enlargement of corn- growing regions, the application of maize hybrids, the increasing use of fertilizers, especially the nitrogenous fertilizer, and a higher growth-density, all have caused a quick spread of sheath blight, the occurring …     

Conditional and unconditional mapping of quantitative trait loci underlying plant height and tiller number in rice (Oryza sativa L.)grown at two nitrogen levels

In this study, we used 127 double haploid (DH) lines to analyze agricultural traits of rice. The DH lines, derived from a ZYQ8 (indica)/JX17 (japonica) cross by anther culture, contained 160 RFLP and 83 SSR markers. Unconditional and conditional quantitative trait loci (QTL) mapping was conducted to analyze plant height (PH) and tillers per plant (TP) at ?ve growth stages that were grown at two nitrogen levels. Fourteen PH and 13 TP unconditional QTL were identified in the di?erent growth stages, including 19 QTL from high-nitrogen (HN) and 14 QTL from low-nitrogen (LN) conditions. The conditional QTL for 14 genomic regions under LN/HN conditions showed that there was a significant effect on PH and TP across the different stages. Only one conditional QTL, ph2-3, was unable to be detected in unconditional mapping. More QTL were detected in the ?rst four rice growth stages than in the final stage. Furthermore, a line from the DH mapping population, DH78, was identified in extreme phenotypes of PH and TP that exhibited dwarfism and less-tiller (dft) characters. The gene dft1 was mapped to chromosome 2 using a backcrossed population of DH78/JX17 through a mapbased cloning strategy. The location of dft1 coincided with the mapping region of the small-LOD peak, QTL ph2 and tp2, which were identified in plants grown in low-nitrogen conditions. Further backcrossing and fine-mapping successfully delimited the dft1 locus to a 91 kb region.     

Conditional and unconditional mapping of quantitative trait loci underlying plant height and tiller number in rice (Oryza sativa L.) grown at two nitrogen levels

In this study,we used 127 double haploid (DH) lines to analyze agricultural traits of rice.The DH lines,derived from a ZYQ8 (indica)/JX17 (japonica) cross by anther culture,contained 160 RFLP and 83 SSR markers.Unconditional and conditional quantitative trait loci (QTL) mapping was conducted to analyze plant height (PH) and tillers per plant (TP) at five growth stages that were grown at two nitrogen levels.Fourteen PH and 13 TP unconditional QTL were identified in the different growth stages,including 19 QTL from high-nitrogen (HN) and 14 QTL from low-nitrogen (LN) conditions.The conditional QTL for 14 genomic regions under LN/HN con-ditions showed that there was a significant effect on PH and TP across the different stages.Only one conditional QTL,ph2-3,was unable to be detected in unconditional mapping.More QTL were detected in the first four rice growth stages than in the final stage.Further-more,a line from the DH mapping population,DH78,was identified in extreme phenotypes of PH and TP that exhibited dwarfism and less-tiller (dft) characters.The gene dftl was mapped to chromosome 2 using a backcrossed population of DH78/JX17 through a map-based cloning strategy.The location of dftl coincided with the mapping region of the small-LOD peak,QTL ph2 and tp2,which were identified in plants grown in low-nitrogen conditions.Further backcrossing and fine-mapping successfully delimited the dftl locus to a 91 kb region.     

Estimation of statistical power and false discovery rate of QTL mapping methods through computer simulation

Many QTL mapping methods have been developed in the past two decades.Statistically,the best method should have a high detection power but a low false discovery rate (FDR).Power and FDR cannot be derived theoretically for most QTL mapping methods,but they can be properly evaluated using computer simulations.In this paper,we used four genetic models (two for independent loci and two for linked loci) to illustrate power and FDR estimation for interval mapping (IM) and inclusive composite interval mapping (ICIM).For each model,we simulated 1000 populations each of 200 doubled haploids.A support interval (SI) was first defined to indicate to which predefined QTL the significant QTL belonged.Power was calculated by counting the number of simulation runs with significant peaks higher than the logarithm of odds (LOD) threshold in the SI.Quantitative trait loci not identified in any SIs were viewed as false positives.The FDR is the rate at which QTLs are identified as significant when they are actually non-significant.Simulation results allowed us to estimate power and FDR of IM and ICIM for two independent and two linkage genetic models.Our estimates allowed us to readily compare the efficiencies of different statistical methods for QTL mapping,including the ability to separate linkage,under a wide range of genetic models.We used IM and ICIM as examples of how to estimate power and FDR,but the principles shown in this paper can be used for power analysis and comparison of any other QTL mapping methods,especially those based on interval tests.     

基于SLAF-seq玉米高密度遗传连锁图谱构建与株型性状QTL定位

 株型直接决定生物产量、种植密度与籽粒产量,利用玉米高密度遗传连锁图谱解析株型相关性状的遗传机制,对选育理想株型玉米新品种具有重要意义。本研究利用SLAF-seq技术,依据玉米黄早四参考基因组信息,对昌7-2与PHB1M及其138个F_2：3家系高通量测序,开发高密度SNP的遗传图谱,并进行株型相关性状QTL定位。研究结果构建了一张总图距为1354.81 cM,标记间的平均距离为0.32 cM,标记数为4220个SLAF标签（7876个SNP）的高密度遗传图谱。在E1与E2两种密度下,对株高、穗位、叶片数、节间数、平均节间长进行QTL定位,共检测到10个QTL位点,其中,有7个PVE超过了10%。叶片数、穗位、节间数为主效QTL,ADD为负值,叶片数与节间数的减效等位基因来源于PHB1M,穗位的减效等位基因来源于昌7-2。叶片数与节间数在2个密度下均定位在8号染色体上,说明二者之间有着共同的遗传机制。与QTL关联的SLAF标记共有61个,其中,SLFA7305498和SLFA6717271为qLC-2-LG8与qIC-2-LG8共有标记。该研究将为玉米株型相关性状的标记辅助选择提供支撑。     

Composite interval mapping of QTL for dynamic traits

The theoretical foundation for mapping quantitative trait loci (QTL) was laid by Sax[1] who discovered the association between the segregation pattern of pigment markers with seed size of bean. However, statistical methods were not well developed until th…     

A new statistical method for mapping QTLs underlying endosperm traits

Genetic expression for an endosperm trait in seeds of cereal crops may be controlled simultaneously by the triploid endosperm genotypes and the diploid maternal genotypes. However, current statistical methods for mapping quantitative trait loci （QTLs） underlying endosperm traits have not been effective in dealing with the putative maternal genetic effects. Combining the quantitative genetic model for diploid maternal traits with triploid endosperm traits, here we propose a new statistical method for mapping QTLs controlling endosperm traits with maternal genetic effects. This method applies the data set of both DNA molecular marker genotypes of each plant in segregation population and the quantitative observations of single endosperms in each plant to map QTL. The maximum likelihood method implemented via the expectation-maximization algorithm was used to the estimate parameters of a putative QTL. Since this method involves the maternal effect that may contribute to endosperm traits, it might be more congruent with the genetics of endosperm traits and more helpful to increasing the precision of QTL mapping. The simulation results show the proposed method provides accurate estimates of the QTL effects and locations with high statistical power.